Posts by Lavorgna Giovanni

... I would like to use the SigCheck package to check the effect of a gene signature on phenotypic data of a dataset of mine. However, I am not sure I understood how to indicate which one are the genes that are over-expressed and those that are instead underexpressedcin in my signature. Could you please ...

... Dear all,
before applying any filter to Exon data, I would like to export them
to a text file as transcripts, i.e, I have RMAed my data using the
following command following the code coming along with the package:
rma.tc.core <- rma(data.exon, "MixExonRMAcore", filedir=outdir,
tmpdir="", backgr ...

... Dear Christian,
many thanks for your further advice on this matter. Next few days, I
will try your workarounds and I'll let you know how things go.
Once again, thanks for your support even late at nights :-)
Giovanni
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Giovanni Lavorgna
D ...

... Dear Christian,
many thanks for your answer and for clarifying matters with the
different ROOT releases.
Yes, before I was using root_v5.26.00 without patch and I can confirm
you that the pipeline you designed without the median-polish
sumamrization ran without problems. However, I tried also the ...

... Dear Christian,
I had the chance to use the whole pipeline you designed and it
performed very well. Basically, I got the probe intensities I was
looking using the whole 185 array dataset. However, if you don't
mind, I have a couple of more questions:
1) I would need to check also the probe intens ...

... Dear Christian,
many thanks for your detailed explanations and the new xps development
version. I couldn't hope for a better support and this is exactly what
I was looking for.
I am currently away from the lab with a slow internet connection and
I couldn't test the whole pipeline you designed. How ...

... Dear Cristian,
many thanks for your prompt answer. In my case, once I have the probe
intensities, I would like to do the following two preliminary steps:
a) Remove probes that hybridize to multiple loci in the genome.
b) Remove probes that show a correlation coefficient below a certain
threshold.
Th ...

...
As you guys know, there is a growing evidence showing that a probe-
level analysis (as opposed to a probeset-level or a gene-level
analysis) could be useful in analyzing Exon arrays. I am currently
analyzing several human exon chips (185!) on a 4 GB machine and I am
using the xps package. I would ...